People

P.I.

Staff

Lab Alumni

Open Standards Compliance

Principle Investigator

Dr. Julia Richards

The research program of
Dr. Julia Richards, PhD
focuses on the underlying causes of hereditary eye disease and the normal processes of ocular aging.
Her research has a long-term emphasis on the group of diseases classified as glaucoma,
one of the leading causes of irreversible blindness in the United States. Several recent breakthroughs
in gene mapping and identification of disease genes, disease risk factors, and risk factors associated
with endophenotypes, have resulted from her collaborations with glaucoma specialists Paul R. Lichter, MD,
Sayoko Moroi, MD, PhD, and Joshua Stein, MD, MS, and biostatistical geneticists Michael Boehnke, PhD,
and Jun Li, PhD, and researchers at other institutions including Stanford, University of Oklahoma, and UCSF.
Over the years she has collaborated with researchers from Ghana, Peru, Australia, Canada, Japan, Korea,
and Taiwan, and more recently has expanded her international collaborations through interaction with the
International Glaucoma Genetics Consortium. She contributed three of the twelve populations in the ten-center
NEIGHBOR genome-wide association study (GWAS) that has led to breakthroughs in identification of common SNPs
associated with open-angle glaucoma its endophenotypes as well as novel pathways associated with glaucoma.

Her work on characterizing specific glaucoma genes and their role in glaucoma and related phenomena is
paralleled by efforts to better understand the clinical characteristics associated with particular genes
and mutations. Studies at the level of genes, cells, animals and people all assist in our efforts to sort
through the underlying causes of the hereditary glaucomas and evaluate the relationships between the
glaucomas and a variety of abnormal developmental processes, both ocular and non-ocular. Linkage analysis,
genome wide association studies, whole exome sequencing, expression profiling all contribute to our search
for the underlying causes of inherited eye disease.

Tools

Software

Madeline

Madeline is a program written by Ed Trager for preparing, visualizing,
and exploring human pedigree data used in genetic linkage studies. Madeline
converts pedigree and marker data into formats required by popular linkage analysis
packages, provides powerful ways to query pedigree data sets, and produces
Postscript pedigree drawings that are useful for rapid data review. We
are pleased to release Madeline under the GNU General Public License (GPL).

Older Versions of Madeline

The stable
version (v. 0.935) now detects simple Mendelian inheritance inconsistencies, provides
publication-quality multipoint LOD score plotting based on the output from programs
like Simwalk2, and features many other improvements.

Madeline v. 0.936 BETA VERSION FOR TESTING DATED 2004.11.04

This new version of Madeline is a bug fix release with some significant improvements as well.
Requires a modern, standards-compliant C++ compiler with a good STL implementation such as
GNU GCC version 3.3 or better. New features include:

Smart table selection allows you to open up data tables without having to specify the
.mfh files. .mfh are created automatically when they don't
exist without having to run recognize manually. Implementation of this feature
has also eliminated some show-stopping segmentation faults.

Directory listing. List files now lists the files in your current working
directory. You need no longer resort to using system "ls -l" as was previously required.

Increased use of C++ STL containers in the code base has resulted in better code, better
memory management, and the elimination of show-stopping bugs.

Despite these improvements, please note that this version is still considered a beta version for
testing until we have been able to test it more extensively. For documentation, please refer
to version 0.935 below.

Shuffle

Shuffle is a utility written by Ed Trager in optimized C++ to randomly shuffle a DNA sequence any number of times.
The program uses a high-quality portable random number generator presented in Press et al.'s
Numerical Recipes in C with a period greater than 2 x 1018. In addition, the program obtains
seeds for the random number generator from an entropy pool present on the compute server.

Gt

Gt is an X11 text file and non-blocking process output viewer written by
Ed Trager. It can be used with Madeline for viewing log files and process output.
Gt may be included as part of the Madeline v. 0.935 distribution.
Requires GTK+ 1.2 libraries.

Edith

Edith is a professional X11 editor for UNIX and Linux platforms
written by Annius V. Groenink that has some particularly nice features for manipulating columns,
highlighting multiple items of data, searching using regular expressions, and other features that are
extremely useful for editing data files. Compared to an editor like vi, Edith has
a much easier learning curve, but still has a fairly extensive set of powerful features useful for advanced data
manipulation.

This editor does not originate from our lab here, but we like it a lot and
highly recommend that you use this program as the editor to use with Madeline.

The Gladiator Project

Gladiator

Gladiator is a new web-based clinical and genetics data entry system being developed
by Ed Trager and Ritu Khanna for joint use in the research labs of Dr.
Anand Swaroop and Dr. Julia Richards here at the Kellogg Eye Center. Although initially designed
for use in these two labs, our long-term goal is to make Gladiator useful for managing
the clinical and genetics data for eye disease studies in general.

Unicode

Unicode Primer

Unicode solves the problem of multiple computer encodings for all of the world's scripts, scientific,
and mathematical
symbols by assigning unique code points in a code space that is much larger than what extended
ASCII could accomodate.
If your work requires that you reach a global audience in one capacity or another, then you'll
want to know about Unicode!

Unicode Font Guide for Free/Libre Open Source Operating Systems

As Linux and the Open Source philosophy and technologies upon which Linux is based have begun to
penetrate new markets
world wide, numerous governmental, non-governmental, commercial, and private organizations
have been collaborating
to provide high-quality Unicode-based fonts to support native language computing.
The following is a selective guide to Unicode-based fonts arranged geographically and by script.
While ideal for use on free/libre Open Source operating systems, these fonts can also be used on
Windows and Mac OSX platforms. This resource is now on unifont.org:

LASi Postscript Printing Engine Project

LASi is a library written by Larry Siden that provides a C++ stream output interface
( with operator << ) for creating Postscript documents that can contain
characters from any of the scripts and symbol blocks supported in
Unicode and by Owen Taylor's
Pango layout engine. The library accomodates right-to-left
scripts such as Arabic and Hebrew as easily as left-to-right scripts. Indic and Indic-derived
Complex Text Layout (CTL) scripts, such as Devanagari, Thai, Lao, and Tibetan are supported
to the extent provided by Pango and by the OpenType fonts installed on your system. All of this
is provided without need for any special configuration or layout calculation on the programmer's part.
LASi is now being maintained by Ed Trager and Ritu Khanna here at the Kellogg Eye Center.

Uv Editor

Uv (Uniview) is a lightweight text editor that supports UTF-8 unicode,
and provides a small set of advanced text and file manipulation abilities.
We decided to start writing Uv after realizing that we were using multiple
different text editors, each for different purposes, because no one text editor provided
all the features we required.

Documentation and Links

Quality Control in the Linkage Analysis Data Pipeline

In February of 2003, Ed Trager gave a talk
to a group of graduate training grant recipients from the Department
of Biostatistics
on quality control issues
and solutions for preparing linkage data for statistical analysis.
This link will take you to the slides used in that presentation.

Richards Lab Bioinformatics Software Documentation

Unix Tutorials

Sooner or later, researchers in the life sciences often need to move beyond the limited world of computing on a
standard Windows PC
and tackle the initially daunting, but in the long run rewarding, world of Unix-based computing.

The following link from the Electronic Engineering Department at the University of Surrey, Guildford, UK,
is a highly recommended "how to" resource that will help you come up to speed on UNIX quickly:

Our link below will provide you with a conceptual overview, as well as in-depth coverage of some of the
more important tools that you will need to know to work in a modern, secure UNIX-based computing environment: